Job ID = 6508740 SRX = SRX467062 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:40:48 prefetch.2.10.7: 1) Downloading 'SRR1164486'... 2020-06-26T14:40:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:44:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:44:16 prefetch.2.10.7: 1) 'SRR1164486' was downloaded successfully Read 44361476 spots for SRR1164486/SRR1164486.sra Written 44361476 spots for SRR1164486/SRR1164486.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:51 44361476 reads; of these: 44361476 (100.00%) were unpaired; of these: 2148730 (4.84%) aligned 0 times 20435631 (46.07%) aligned exactly 1 time 21777115 (49.09%) aligned >1 times 95.16% overall alignment rate Time searching: 00:17:51 Overall time: 00:17:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 22037494 / 42212746 = 0.5221 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 27 Jun 2020 00:11:40: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:11:40: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:11:46: 1000000 INFO @ Sat, 27 Jun 2020 00:11:51: 2000000 INFO @ Sat, 27 Jun 2020 00:11:56: 3000000 INFO @ Sat, 27 Jun 2020 00:12:02: 4000000 INFO @ Sat, 27 Jun 2020 00:12:07: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 27 Jun 2020 00:12:10: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:12:10: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:12:13: 6000000 INFO @ Sat, 27 Jun 2020 00:12:16: 1000000 INFO @ Sat, 27 Jun 2020 00:12:19: 7000000 INFO @ Sat, 27 Jun 2020 00:12:22: 2000000 INFO @ Sat, 27 Jun 2020 00:12:25: 8000000 INFO @ Sat, 27 Jun 2020 00:12:28: 3000000 INFO @ Sat, 27 Jun 2020 00:12:31: 9000000 INFO @ Sat, 27 Jun 2020 00:12:34: 4000000 INFO @ Sat, 27 Jun 2020 00:12:37: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 27 Jun 2020 00:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 27 Jun 2020 00:12:40: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:12:40: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:12:40: 5000000 INFO @ Sat, 27 Jun 2020 00:12:43: 11000000 INFO @ Sat, 27 Jun 2020 00:12:46: 1000000 INFO @ Sat, 27 Jun 2020 00:12:47: 6000000 INFO @ Sat, 27 Jun 2020 00:12:49: 12000000 INFO @ Sat, 27 Jun 2020 00:12:52: 2000000 INFO @ Sat, 27 Jun 2020 00:12:53: 7000000 INFO @ Sat, 27 Jun 2020 00:12:55: 13000000 INFO @ Sat, 27 Jun 2020 00:12:58: 3000000 INFO @ Sat, 27 Jun 2020 00:12:59: 8000000 INFO @ Sat, 27 Jun 2020 00:13:01: 14000000 INFO @ Sat, 27 Jun 2020 00:13:04: 4000000 INFO @ Sat, 27 Jun 2020 00:13:05: 9000000 INFO @ Sat, 27 Jun 2020 00:13:07: 15000000 INFO @ Sat, 27 Jun 2020 00:13:10: 5000000 INFO @ Sat, 27 Jun 2020 00:13:10: 10000000 INFO @ Sat, 27 Jun 2020 00:13:13: 16000000 INFO @ Sat, 27 Jun 2020 00:13:16: 6000000 INFO @ Sat, 27 Jun 2020 00:13:17: 11000000 INFO @ Sat, 27 Jun 2020 00:13:19: 17000000 INFO @ Sat, 27 Jun 2020 00:13:22: 7000000 INFO @ Sat, 27 Jun 2020 00:13:23: 12000000 INFO @ Sat, 27 Jun 2020 00:13:25: 18000000 INFO @ Sat, 27 Jun 2020 00:13:28: 8000000 INFO @ Sat, 27 Jun 2020 00:13:29: 13000000 INFO @ Sat, 27 Jun 2020 00:13:31: 19000000 INFO @ Sat, 27 Jun 2020 00:13:34: 9000000 INFO @ Sat, 27 Jun 2020 00:13:35: 14000000 INFO @ Sat, 27 Jun 2020 00:13:37: 20000000 INFO @ Sat, 27 Jun 2020 00:13:38: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:13:38: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:13:38: #1 total tags in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:13:38: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:13:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:13:39: #1 tags after filtering in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:13:39: #1 finished! INFO @ Sat, 27 Jun 2020 00:13:39: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:13:40: #2 number of paired peaks: 883 WARNING @ Sat, 27 Jun 2020 00:13:40: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 27 Jun 2020 00:13:40: start model_add_line... INFO @ Sat, 27 Jun 2020 00:13:40: start X-correlation... INFO @ Sat, 27 Jun 2020 00:13:40: end of X-cor INFO @ Sat, 27 Jun 2020 00:13:40: #2 finished! INFO @ Sat, 27 Jun 2020 00:13:40: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:13:40: #2 alternative fragment length(s) may be 1,567,598 bps INFO @ Sat, 27 Jun 2020 00:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05_model.r WARNING @ Sat, 27 Jun 2020 00:13:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:13:40: #2 You may need to consider one of the other alternative d(s): 1,567,598 WARNING @ Sat, 27 Jun 2020 00:13:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:13:40: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:13:40: 10000000 INFO @ Sat, 27 Jun 2020 00:13:41: 15000000 INFO @ Sat, 27 Jun 2020 00:13:46: 11000000 INFO @ Sat, 27 Jun 2020 00:13:47: 16000000 INFO @ Sat, 27 Jun 2020 00:13:52: 12000000 INFO @ Sat, 27 Jun 2020 00:13:53: 17000000 INFO @ Sat, 27 Jun 2020 00:13:58: 13000000 INFO @ Sat, 27 Jun 2020 00:13:59: 18000000 INFO @ Sat, 27 Jun 2020 00:14:04: 14000000 INFO @ Sat, 27 Jun 2020 00:14:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:14:11: 15000000 INFO @ Sat, 27 Jun 2020 00:14:11: 20000000 INFO @ Sat, 27 Jun 2020 00:14:13: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:14:13: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:14:13: #1 total tags in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:14:13: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:14:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:14:13: #1 tags after filtering in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:14:13: #1 finished! INFO @ Sat, 27 Jun 2020 00:14:13: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:14:15: #2 number of paired peaks: 883 WARNING @ Sat, 27 Jun 2020 00:14:15: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 27 Jun 2020 00:14:15: start model_add_line... INFO @ Sat, 27 Jun 2020 00:14:15: start X-correlation... INFO @ Sat, 27 Jun 2020 00:14:15: end of X-cor INFO @ Sat, 27 Jun 2020 00:14:15: #2 finished! INFO @ Sat, 27 Jun 2020 00:14:15: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:14:15: #2 alternative fragment length(s) may be 1,567,598 bps INFO @ Sat, 27 Jun 2020 00:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10_model.r WARNING @ Sat, 27 Jun 2020 00:14:15: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:14:15: #2 You may need to consider one of the other alternative d(s): 1,567,598 WARNING @ Sat, 27 Jun 2020 00:14:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:14:15: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:14:16: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:14:17: 16000000 INFO @ Sat, 27 Jun 2020 00:14:23: 17000000 INFO @ Sat, 27 Jun 2020 00:14:29: 18000000 INFO @ Sat, 27 Jun 2020 00:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.05_summits.bed INFO @ Sat, 27 Jun 2020 00:14:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:14:34: 19000000 INFO @ Sat, 27 Jun 2020 00:14:40: 20000000 INFO @ Sat, 27 Jun 2020 00:14:41: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:14:41: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:14:41: #1 total tags in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:14:41: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:14:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:14:42: #1 tags after filtering in treatment: 20175252 INFO @ Sat, 27 Jun 2020 00:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:14:42: #1 finished! INFO @ Sat, 27 Jun 2020 00:14:42: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:14:43: #2 number of paired peaks: 883 WARNING @ Sat, 27 Jun 2020 00:14:43: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 27 Jun 2020 00:14:43: start model_add_line... INFO @ Sat, 27 Jun 2020 00:14:43: start X-correlation... INFO @ Sat, 27 Jun 2020 00:14:43: end of X-cor INFO @ Sat, 27 Jun 2020 00:14:43: #2 finished! INFO @ Sat, 27 Jun 2020 00:14:43: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:14:43: #2 alternative fragment length(s) may be 1,567,598 bps INFO @ Sat, 27 Jun 2020 00:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20_model.r WARNING @ Sat, 27 Jun 2020 00:14:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:14:43: #2 You may need to consider one of the other alternative d(s): 1,567,598 WARNING @ Sat, 27 Jun 2020 00:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:14:43: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:14:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.10_summits.bed INFO @ Sat, 27 Jun 2020 00:15:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:15:19: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467062/SRX467062.20_summits.bed INFO @ Sat, 27 Jun 2020 00:15:35: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling